# A tibble: 618 × 20
Genome Genome_type Length N_contigs N50 GC_content Completeness
<chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 MGYG000303700 MAG 678213 2 466332 47.8 63.7
2 MGYG000303701 MAG 1500176 18 112881 42.4 87.8
3 MGYG000303702 MAG 1210062 44 48790 26.4 94.8
4 MGYG000303703 MAG 1706016 27 89653 44.6 93.7
5 MGYG000303704 MAG 703182 7 111709 47.8 63.7
6 MGYG000303705 MAG 2542045 112 34925 48 97.9
7 MGYG000303706 MAG 1449687 185 10153 34.8 85.2
8 MGYG000303707 MAG 1874692 90 28768 37.1 99.0
9 MGYG000303708 MAG 1480380 12 169949 42.2 87.6
10 MGYG000303709 MAG 694644 57 15063 47.9 62.0
# ℹ 608 more rows
# ℹ 13 more variables: Contamination <dbl>, rRNA_5S <dbl>, rRNA_16S <dbl>,
# rRNA_23S <dbl>, tRNAs <dbl>, Genome_accession <chr>, Species_rep <chr>,
# Lineage <chr>, Sample_accession <chr>, Study_accession <chr>,
# Country <chr>, Continent <chr>, FTP_download <chr>Exploring meta-data of human vaginal microbiome
Group 6
DATA DESCRIPTION
- 618 vaginal metagenome-assembled genomes (MAGs)
- 25 variables covering taxonomy, assembly quality, and geography
- High completeness and low contamination for most genomes
- Dataset dominated by a few major bacterial phyla
- Genome lengths fall within biologically expected ranges
Most MAGs belong to only a few dominant phyla.
This indicates strong taxonomic skew in the dataset.
Most genomes have high completeness (>90%),
indicating generally strong assembly quality.
Genome lengths fall within the expected biological range
for vaginal bacterial taxa (typically 1.5–3 Mb).
ANALYSIS 1 - Phylogenetic tree
- Constructed a phylogenetic tree from the taxonomic ranks (Domain → Species) in the augmented dataset.
- NA values in taxonomy were removed before tree construction.
- The tree is colored by phylum to show taxonomic clustering.
ANALYSIS 2 - Data quality
Investigating the quality of samples.
- Scatterplot of completeness (%) vs. contamination (%) for all MAGs
- The dashed lines mark the high-quality genomes (above 90% completeness and below 5% contamination)
- Points are colored by phylum
- Most MAGs cluster in the high-quality area indicating good assemble quality of the MAGs.
ANALYSIS 3 - Associated and non-associated-endometriosis MAGs
- Compared endometriosis-associated vs non-associated MAGs
- Focused on GC content, genome length, completeness & contamination
- Investigated whether associated MAGs cluster taxonomically
- Goal: determine if associated MAGs form a genomically distinct group
Endometriosis-associated MAGs occur in only a few phyla.
Most phyla contain no associated MAGs, suggesting limited taxonomic clustering.
GC content ranges overlap almost completely.
No evidence that GC% distinguishes associated vs non-associated MAGs.
ANALYSIS 4 - Species Distribution between countries
- Investigating the distribution of lineage groups in Countries
- Counted group instances for each country and wide format
- Filtered for NA in Countries
- Big difference in sample size –> normalize
Some variation between countries. I.e. Order Bacteroidales, but not much.
Could’ve tested for significance.
Only two principal components –> 100% variance.
Clear division of countries.
Along PC1, Fusobacteria and Bacteroidota (order = Bacteroidales). Correlation with heatmap.
Test to see if there is a significant difference in the proportion of endometriosis-associated genomes between countries
| country1 | country2 | p_value | odds_ratio | CI_low | CI_high |
|---|---|---|---|---|---|
| USA | China | 0.0205 | 2.670 | 1.113 | 7.779 |
| USA | Denmark | 0.1554 | 4.648 | 0.738 | 193.498 |
| Denmark | China | 1.0000 | 0.576 | 0.012 | 5.077 |
- Significant difference between USA and China
- USA displayed 2.7 times higher odds of endometriosis-associated genomes
- No significant difference between USA vs. Denmark or Denmark vs. China
- Likely due to the limited amount of danish and chinese genomes represented